Buggy code:
public class PopulateNeuroMLModelTreeUtils { private NeuroMLAccessUtility neuroMLAccessUtility = new NeuroMLAccessUtility ( ) ; private ModelWrapper model ; public ModelWrapper getModel ( ) { } public void setModel ( ModelWrapper model ) { } public CompositeNode createRateGateNode ( Resources name , HHRate rate ) throws ModelInterpreterException , ContentError { } public CompositeNode createSteadyStateNode ( HHVariable variable ) throws ModelInterpreterException , ContentError { } public CompositeNode createTimeCourseNode ( HHTime timeCourse ) throws ModelInterpreterException , ContentError { } public CompositeNode createCellNode ( BaseCell c ) throws ModelInterpreterException , ContentError { } public Collection < ParameterSpecificationNode > createBasePyNNIaFCellChildren ( BasePyNNIaFCell c ) { } public Collection < ParameterSpecificationNode > createBasePyNNCellChildren ( BasePyNNCell c ) { } public CompositeNode createBiophysicalPropertiesNode ( BiophysicalProperties properties ) throws ModelInterpreterException , ContentError { } private CompositeNode createVariableParameterNode ( List < VariableParameter > variableParameters ) { } public CompositeNode createIntracellularPropertiesNode ( IntracellularProperties intracellularProperties ) throws ModelInterpreterException { } public CompositeNode createExtracellularPropertiesNode ( ExtracellularProperties extracellularProperties ) throws ModelInterpreterException { } private List < CompositeNode > createSpeciesNode ( List < Species > species ) throws ModelInterpreterException { List < CompositeNode > speciesNodeList = new ArrayList < CompositeNode > ( ) ; for ( Species specie : species ) { <START_BUG> CompositeNode speciesNodeItem = new CompositeNode ( specie . getId ( ) , PopulateGeneralModelTreeUtils . getUniqueName ( SPECIES . get ( ) , specie ) ) ; <END_BUG> speciesNodeItem . addChild ( PopulateNodesModelTreeUtils . createParameterSpecificationNode ( INIT_CONCENTRATION . getId ( ) , INIT_CONCENTRATION . get ( ) , specie . getInitialConcentration ( ) ) ) ; speciesNodeItem . addChild ( PopulateNodesModelTreeUtils . createParameterSpecificationNode ( INIT_EXT_CONCENTRATION . getId ( ) , INIT_EXT_CONCENTRATION . get ( ) , specie . getInitialExtConcentration ( ) ) ) ; speciesNodeItem . addChild ( PopulateNodesModelTreeUtils . createTextMetadataNode ( ION . getId ( ) , ION . get ( ) , new org . geppetto . core . model . values . StringValue ( specie . getIon ( ) ) ) ) ; speciesNodeItem . addChild ( createConcentrationModelNode ( neuroMLAccessUtility . getComponent ( specie . getConcentrationModel ( ) , model , CONCENTRATION_MODEL ) ) ) ; speciesNodeList . add ( speciesNodeItem ) ; } return speciesNodeList ; } public CompositeNode createConcentrationModelNode ( Object concentrationModel ) { } public CompositeNode createGateNode ( Base gate ) throws ModelInterpreterException , ContentError { } private CompositeNode createQ10SettingsNode ( Q10Settings q10Settings ) throws ModelInterpreterException , ContentError { } public CompositeNode createChannelNode ( IonChannel ionChannelBase ) throws ModelInterpreterException , ContentError { } public Collection < ParameterSpecificationNode > createIafTauCellChildren ( IafTauCell c ) { } public Collection < ParameterSpecificationNode > createIafCellChildren ( IafCell c ) { } public CompositeNode createNetworkNode ( Network n ) throws ModelInterpreterException , ContentError { } public CompositeNode createSynapseNode ( BaseConductanceBasedSynapse synapse ) throws ModelInterpreterException , ContentError { } public CompositeNode createPynnSynapseNode ( BasePynnSynapse pynnSynapse ) throws ModelInterpreterException , ContentError { } public Collection < ANode > createExpTwoSynapseChildren ( ExpTwoSynapse expTwoSynapse ) { } public Collection < ANode > createStandaloneChildren ( Standalone standaloneComponent ) { } private CompositeNode createAnnotationChild ( Node subNode ) { } public Collection < ANode > createBaseChildren ( Base baseComponent ) { } public List < ANode > createInfoNode ( InfoNode infoNode ) throws ModelInterpreterException { } }

Fix:
CompositeNode speciesNodeItem = new CompositeNode ( specie . getId ( ) , PopulateGeneralModelTreeUtils . getUniqueName ( SPECIES . get ( ) , specie . getId ( ) ) ) ;